LAMMPS (8 Mar 2018)
  using 1 OpenMP thread(s) per MPI task
# Initialization
units           metal
boundary        p p p
atom_style      atomic
processors      * * 1     # domain decomposition over x and y

# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# interactions can be specified separately
read_data       data.graphene-adsorbant   # read lammps data file
  orthogonal box = (0 0 -10) to (17.04 19.6761 40)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  129 atoms
mass            1 12.0107   # carbon mass (g/mole) | membrane
mass            2 12.0107   # carbon mass (g/mole) | adsorbate
# Neighbor update settings
neighbor        2.0 bin
neigh_modify    every 1
neigh_modify    delay 0
neigh_modify    check yes
# Separate atom groups
group membrane  type 1
128 atoms in group membrane
group adsorbant type 2
1 atoms in group adsorbant

######################## Potential defition ########################
pair_style  hybrid/overlay  kolmogorov/crespi/z 14.0
####################################################################
pair_coeff * * none
pair_coeff 1 2 kolmogorov/crespi/z  CC.KC   C C  # long-range
####################################################################

#### Simulation settings ####
timestep  0.0001
fix       thermostat adsorbant nve
fix       rigid_membrane membrane setforce 0 0 0
compute   COM1 membrane  com
compute   COM2 adsorbant com
############################

# Output
#dump            1 all xyz 100 trajec.xyz
#dump_modify     1 format line "%s %12.6f %12.6f %12.6f" element "C" "C"
thermo          100
thermo_style    custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu
thermo_modify   line one format float %14.8f

###### Run molecular dynamics ######
run 10000
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 16
  ghost atom cutoff = 16
  binsize = 8, bins = 3 3 7
  2 neighbor lists, perpetual/occasional/extra = 2 0 0
  (1) pair kolmogorov/crespi/z, perpetual, skip from (2)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
  (2) neighbor class addition, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.206 | 3.206 | 3.206 Mbytes
Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3] 
       0     0.00000000    -0.02562011    -0.02562011     0.00000000     0.00000000     3.30000000 
     100     0.01000000    -0.02562011    -0.02584808     0.01377831     0.00000000     3.30302413 
     200     0.02000000    -0.02562011    -0.02650010     0.05318658     0.00000000     3.31198892 
     300     0.03000000    -0.02562011    -0.02748822     0.11290898     0.00000000     3.32658305 
     400     0.04000000    -0.02562011    -0.02868854     0.18545625     0.00000000     3.34632324 
     500     0.05000000    -0.02562011    -0.02996656     0.26269978     0.00000000     3.37059992 
     600     0.06000000    -0.02562011    -0.03120006     0.33725276     0.00000000     3.39872815 
     700     0.07000000    -0.02562011    -0.03229421     0.40338328     0.00000000     3.42999603 
     800     0.08000000    -0.02562011    -0.03318758     0.45737874     0.00000000     3.46370507 
     900     0.09000000    -0.02562011    -0.03385069     0.49745690     0.00000000     3.49919977 
    1000     0.10000000    -0.02562011    -0.03428002     0.52340564     0.00000000     3.53588638 
    1100     0.11000000    -0.02562011    -0.03449041     0.53612164     0.00000000     3.57324216 
    1200     0.12000000    -0.02562011    -0.03450775     0.53717016     0.00000000     3.61081749 
    1300     0.13000000    -0.02562011    -0.03436312     0.52842859     0.00000000     3.64823296 
    1400     0.14000000    -0.02562011    -0.03408851     0.51183115     0.00000000     3.68517357 
    1500     0.15000000    -0.02562011    -0.03371417     0.48920613     0.00000000     3.72138134 
    1600     0.16000000    -0.02562011    -0.03326714     0.46218758     0.00000000     3.75664759 
    1700     0.17000000    -0.02562011    -0.03277063     0.43217815     0.00000000     3.79080541 
    1800     0.18000000    -0.02562011    -0.03224395     0.40034589     0.00000000     3.82372274 
    1900     0.19000000    -0.02562011    -0.03170282     0.36763982     0.00000000     3.85529629 
    2000     0.20000000    -0.02562011    -0.03115972     0.33481494     0.00000000     3.88544626 
    2100     0.21000000    -0.02562011    -0.03062440     0.30246010     0.00000000     3.91411185 
    2200     0.22000000    -0.02562011    -0.03010433     0.27102702     0.00000000     3.94124749 
    2300     0.23000000    -0.02562011    -0.02960514     0.24085558     0.00000000     3.96681976 
    2400     0.24000000    -0.02562011    -0.02913096     0.21219623     0.00000000     3.99080483 
    2500     0.25000000    -0.02562011    -0.02868478     0.18522907     0.00000000     4.01318637 
    2600     0.26000000    -0.02562011    -0.02826867     0.16007955     0.00000000     4.03395384 
    2700     0.27000000    -0.02562011    -0.02788403     0.13683143     0.00000000     4.05310113 
    2800     0.28000000    -0.02562011    -0.02753171     0.11553708     0.00000000     4.07062542 
    2900     0.29000000    -0.02562011    -0.02721220     0.09622581     0.00000000     4.08652629 
    3000     0.30000000    -0.02562011    -0.02692571     0.07891041     0.00000000     4.10080498 
    3100     0.31000000    -0.02562011    -0.02667226     0.06359229     0.00000000     4.11346382 
    3200     0.32000000    -0.02562011    -0.02645177     0.05026555     0.00000000     4.12450573 
    3300     0.33000000    -0.02562011    -0.02626406     0.03892009     0.00000000     4.13393390 
    3400     0.34000000    -0.02562011    -0.02610893     0.02954399     0.00000000     4.14175142 
    3500     0.35000000    -0.02562011    -0.02598618     0.02212545     0.00000000     4.14796110 
    3600     0.36000000    -0.02562011    -0.02589566     0.01665409     0.00000000     4.15256529 
    3700     0.37000000    -0.02562011    -0.02583722     0.01312208     0.00000000     4.15556569 
    3800     0.38000000    -0.02562011    -0.02581079     0.01152492     0.00000000     4.15696329 
    3900     0.39000000    -0.02562011    -0.02581636     0.01186148     0.00000000     4.15675830 
    4000     0.40000000    -0.02562011    -0.02585398     0.01413478     0.00000000     4.15495012 
    4100     0.41000000    -0.02562011    -0.02592375     0.01835185     0.00000000     4.15153731 
    4200     0.42000000    -0.02562011    -0.02602587     0.02452390     0.00000000     4.14651764 
    4300     0.43000000    -0.02562011    -0.02616057     0.03266513     0.00000000     4.13988811 
    4400     0.44000000    -0.02562011    -0.02632813     0.04279292     0.00000000     4.13164506 
    4500     0.45000000    -0.02562011    -0.02652889     0.05492664     0.00000000     4.12178432 
    4600     0.46000000    -0.02562011    -0.02676317     0.06908643     0.00000000     4.11030130 
    4700     0.47000000    -0.02562011    -0.02703129     0.08529164     0.00000000     4.09719124 
    4800     0.48000000    -0.02562011    -0.02733352     0.10355859     0.00000000     4.08244950 
    4900     0.49000000    -0.02562011    -0.02767004     0.12389788     0.00000000     4.06607186 
    5000     0.50000000    -0.02562011    -0.02804086     0.14631034     0.00000000     4.04805502 
    5100     0.51000000    -0.02562011    -0.02844575     0.17078211     0.00000000     4.02839708 
    5200     0.52000000    -0.02562011    -0.02888415     0.19727899     0.00000000     4.00709829 
    5300     0.53000000    -0.02562011    -0.02935502     0.22573844     0.00000000     3.98416189 
    5400     0.54000000    -0.02562011    -0.02985670     0.25605986     0.00000000     3.95959511 
    5500     0.55000000    -0.02562011    -0.03038669     0.28809268     0.00000000     3.93341053 
    5600     0.56000000    -0.02562011    -0.03094143     0.32162137     0.00000000     3.90562766 
    5700     0.57000000    -0.02562011    -0.03151597     0.35634628     0.00000000     3.87627492 
    5800     0.58000000    -0.02562011    -0.03210361     0.39186361     0.00000000     3.84539210 
    5900     0.59000000    -0.02562011    -0.03269556     0.42764084     0.00000000     3.81303330 
    6000     0.60000000    -0.02562011    -0.03328042     0.46299030     0.00000000     3.77927044 
    6100     0.61000000    -0.02562011    -0.03384380     0.49704060     0.00000000     3.74419758 
    6200     0.62000000    -0.02562011    -0.03436783     0.52871353     0.00000000     3.70793588 
    6300     0.63000000    -0.02562011    -0.03483104     0.55670974     0.00000000     3.67063945 
    6400     0.64000000    -0.02562011    -0.03520832     0.57951248     0.00000000     3.63250187 
    6500     0.65000000    -0.02562011    -0.03547159     0.59542438     0.00000000     3.59376331 
    6600     0.66000000    -0.02562011    -0.03559125     0.60265655     0.00000000     3.55471782 
    6700     0.67000000    -0.02562011    -0.03553879     0.59948637     0.00000000     3.51572023 
    6800     0.68000000    -0.02562011    -0.03529110     0.58451568     0.00000000     3.47719153 
    6900     0.69000000    -0.02562011    -0.03483635     0.55703035     0.00000000     3.43962129 
    7000     0.70000000    -0.02562011    -0.03418150     0.51745146     0.00000000     3.40356509 
    7100     0.71000000    -0.02562011    -0.03336032     0.46781889     0.00000000     3.36963482 
    7200     0.72000000    -0.02562011    -0.03243997     0.41219328     0.00000000     3.33847933 
    7300     0.73000000    -0.02562011    -0.03152342     0.35679665     0.00000000     3.31075400 
    7400     0.74000000    -0.02562011    -0.03074422     0.30970201     0.00000000     3.28707906 
    7500     0.75000000    -0.02562011    -0.03025182     0.27994115     0.00000000     3.26798907 
    7600     0.76000000    -0.02562011    -0.03018799     0.27608346     0.00000000     3.25387900 
    7700     0.77000000    -0.02562011    -0.03065928     0.30456818     0.00000000     3.24495492 
    7800     0.78000000    -0.02562011    -0.03171321     0.36826788     0.00000000     3.24119821 
    7900     0.79000000    -0.02562011    -0.03332635     0.46576624     0.00000000     3.24235091 
    8000     0.80000000    -0.02562011    -0.03540847     0.59160963     0.00000000     3.24792582 
    8100     0.81000000    -0.02562011    -0.03782107     0.73742737     0.00000000     3.25723999 
    8200     0.82000000    -0.02562011    -0.04040358     0.89351498     0.00000000     3.26946524 
    8300     0.83000000    -0.02562011    -0.04299943     1.05040805     0.00000000     3.28368734 
    8400     0.84000000    -0.02562011    -0.04547588     1.20008497     0.00000000     3.29896495 
    8500     0.85000000    -0.02562011    -0.04773539     1.33664998     0.00000000     3.31438148 
    8600     0.86000000    -0.02562011    -0.04971913     1.45654768     0.00000000     3.32908572 
    8700     0.87000000    -0.02562011    -0.05140498     1.55844058     0.00000000     3.34231951 
    8800     0.88000000    -0.02562011    -0.05280154     1.64284923     0.00000000     3.35343297 
    8900     0.89000000    -0.02562011    -0.05394019     1.71166905     0.00000000     3.36188901 
    9000     0.90000000    -0.02562011    -0.05486563     1.76760281     0.00000000     3.36725955 
    9100     0.91000000    -0.02562011    -0.05562624     1.81357448     0.00000000     3.36921674 
    9200     0.92000000    -0.02562011    -0.05626439     1.85214388     0.00000000     3.36752214 
    9300     0.93000000    -0.02562011    -0.05680723     1.88495335     0.00000000     3.36201704 
    9400     0.94000000    -0.02562011    -0.05725852     1.91222952     0.00000000     3.35261669 
    9500     0.95000000    -0.02562011    -0.05759110     1.93233038     0.00000000     3.33931122 
    9600     0.96000000    -0.02562011    -0.05774152     1.94142215     0.00000000     3.32217490 
    9700     0.97000000    -0.02562011    -0.05760814     1.93336063     0.00000000     3.30138553 
    9800     0.98000000    -0.02562012    -0.05705439     1.89989139     0.00000000     3.27725394 
    9900     0.99000000    -0.02562012    -0.05592079     1.83137685     0.00000000     3.25026233 
   10000     1.00000000    -0.02562012    -0.05404919     1.71825669     0.00000000     3.22110695 
Loop time of 0.34689 on 1 procs for 10000 steps with 129 atoms

Performance: 249.070 ns/day, 0.096 hours/ns, 28827.585 timesteps/s
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.2028     | 0.2028     | 0.2028     |   0.0 | 58.46
Neigh   | 0.00021529 | 0.00021529 | 0.00021529 |   0.0 |  0.06
Comm    | 0.10656    | 0.10656    | 0.10656    |   0.0 | 30.72
Output  | 0.0015109  | 0.0015109  | 0.0015109  |   0.0 |  0.44
Modify  | 0.011605   | 0.011605   | 0.011605   |   0.0 |  3.35
Other   |            | 0.0242     |            |       |  6.98

Nlocal:    129 ave 129 max 129 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    1867 ave 1867 max 1867 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    290 ave 290 max 290 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 290
Ave neighs/atom = 2.24806
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:00
